Multiple sequence alignment - TraesCS2A01G119900

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS2A01G119900 chr2A 100.000 2898 0 0 1 2898 70192262 70195159 0.000000e+00 5352.0
1 TraesCS2A01G119900 chr2A 75.821 670 93 38 753 1385 70654815 70655452 2.840000e-70 276.0
2 TraesCS2A01G119900 chr2A 83.122 237 23 10 750 983 70643749 70643971 1.760000e-47 200.0
3 TraesCS2A01G119900 chr2D 91.897 2209 96 32 711 2898 71391103 71393249 0.000000e+00 3011.0
4 TraesCS2A01G119900 chr2D 87.727 1597 122 26 681 2231 70796709 70795141 0.000000e+00 1796.0
5 TraesCS2A01G119900 chr2D 94.925 335 14 3 1 333 71390767 71391100 3.310000e-144 521.0
6 TraesCS2A01G119900 chr2D 77.064 436 78 15 971 1386 71594218 71594651 6.250000e-57 231.0
7 TraesCS2A01G119900 chr2D 80.417 240 25 12 755 992 71565428 71565647 2.310000e-36 163.0
8 TraesCS2A01G119900 chr2D 86.713 143 12 4 750 892 71578109 71578244 5.000000e-33 152.0
9 TraesCS2A01G119900 chr2D 88.298 94 9 2 743 836 71382377 71382468 8.490000e-21 111.0
10 TraesCS2A01G119900 chr2B 91.353 1966 101 25 755 2696 107531444 107533364 0.000000e+00 2625.0
11 TraesCS2A01G119900 chr2B 89.085 852 78 4 1382 2231 107081398 107080560 0.000000e+00 1044.0
12 TraesCS2A01G119900 chr2B 86.743 611 62 7 747 1356 107085508 107084916 0.000000e+00 662.0
13 TraesCS2A01G119900 chr2B 95.930 172 7 0 2727 2898 107533364 107533535 2.200000e-71 279.0
14 TraesCS2A01G119900 chr2B 77.670 515 56 29 747 1222 107576681 107577175 2.860000e-65 259.0
15 TraesCS2A01G119900 chr2B 78.545 275 33 11 99 356 107520472 107520737 1.080000e-34 158.0
16 TraesCS2A01G119900 chr2B 91.964 112 9 0 1809 1920 107521533 107521644 1.080000e-34 158.0
17 TraesCS2A01G119900 chr2B 81.347 193 17 12 750 940 107782944 107783119 3.890000e-29 139.0
18 TraesCS2A01G119900 chr2B 94.828 58 3 0 623 680 107521115 107521172 1.110000e-14 91.6


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2A01G119900 chr2A 70192262 70195159 2897 False 5352 5352 100.0000 1 2898 1 chr2A.!!$F1 2897
1 TraesCS2A01G119900 chr2A 70654815 70655452 637 False 276 276 75.8210 753 1385 1 chr2A.!!$F3 632
2 TraesCS2A01G119900 chr2D 70795141 70796709 1568 True 1796 1796 87.7270 681 2231 1 chr2D.!!$R1 1550
3 TraesCS2A01G119900 chr2D 71390767 71393249 2482 False 1766 3011 93.4110 1 2898 2 chr2D.!!$F5 2897
4 TraesCS2A01G119900 chr2B 107531444 107533535 2091 False 1452 2625 93.6415 755 2898 2 chr2B.!!$F4 2143
5 TraesCS2A01G119900 chr2B 107080560 107085508 4948 True 853 1044 87.9140 747 2231 2 chr2B.!!$R1 1484

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
892 908 0.106719 TTCCTCGCCAATCCCCATTC 60.107 55.0 0.0 0.0 0.0 2.67 F
894 910 1.103398 CCTCGCCAATCCCCATTCAC 61.103 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1693 5273 0.249657 GCAGGATGAAGGGCGTAGAG 60.250 60.0 0.0 0.0 39.69 2.43 R
2664 6270 0.773644 AGCATGTGTCCTCCAAAGGT 59.226 50.0 0.0 0.0 43.82 3.50 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.422204 AGGGCGCCCTCCAATTAA 58.578 55.556 42.84 0.00 44.43 1.40
37 38 3.195610 GCCCTCCAATTAAAAGTTCCCAG 59.804 47.826 0.00 0.00 0.00 4.45
59 60 7.285401 CCCAGCTAACAGTAAAATCAACCATAT 59.715 37.037 0.00 0.00 0.00 1.78
163 165 5.767816 GAAAAACCCTTTTCTCACTAGCA 57.232 39.130 3.63 0.00 44.73 3.49
232 235 7.359765 GCATTCTGCAACCAATATTCAATATGC 60.360 37.037 0.00 0.00 44.26 3.14
239 242 7.492020 GCAACCAATATTCAATATGCTGTTTGA 59.508 33.333 4.38 0.00 0.00 2.69
289 292 9.434559 GGCTAACAATTCGAATACTAACATTTC 57.565 33.333 11.83 0.00 0.00 2.17
329 332 7.707104 ACTTTAATTTCAGAATCCCTATTGCG 58.293 34.615 0.00 0.00 0.00 4.85
333 336 5.756195 TTTCAGAATCCCTATTGCGATTG 57.244 39.130 0.00 0.00 0.00 2.67
335 338 4.780815 TCAGAATCCCTATTGCGATTGTT 58.219 39.130 0.00 0.00 0.00 2.83
336 339 5.924356 TCAGAATCCCTATTGCGATTGTTA 58.076 37.500 0.00 0.00 0.00 2.41
337 340 6.533730 TCAGAATCCCTATTGCGATTGTTAT 58.466 36.000 0.00 0.00 0.00 1.89
338 341 7.676004 TCAGAATCCCTATTGCGATTGTTATA 58.324 34.615 0.00 0.00 0.00 0.98
339 342 8.154203 TCAGAATCCCTATTGCGATTGTTATAA 58.846 33.333 0.00 0.00 0.00 0.98
340 343 8.783093 CAGAATCCCTATTGCGATTGTTATAAA 58.217 33.333 0.00 0.00 0.00 1.40
341 344 9.003658 AGAATCCCTATTGCGATTGTTATAAAG 57.996 33.333 0.00 0.00 0.00 1.85
342 345 8.691661 AATCCCTATTGCGATTGTTATAAAGT 57.308 30.769 0.00 0.00 0.00 2.66
343 346 8.691661 ATCCCTATTGCGATTGTTATAAAGTT 57.308 30.769 0.00 0.00 0.00 2.66
344 347 9.787435 ATCCCTATTGCGATTGTTATAAAGTTA 57.213 29.630 0.00 0.00 0.00 2.24
345 348 9.616156 TCCCTATTGCGATTGTTATAAAGTTAA 57.384 29.630 0.00 0.00 0.00 2.01
346 349 9.659830 CCCTATTGCGATTGTTATAAAGTTAAC 57.340 33.333 0.00 0.00 33.56 2.01
350 353 9.783256 ATTGCGATTGTTATAAAGTTAACTTCC 57.217 29.630 20.78 7.85 34.61 3.46
351 354 8.325421 TGCGATTGTTATAAAGTTAACTTCCA 57.675 30.769 20.78 12.36 34.61 3.53
352 355 8.784994 TGCGATTGTTATAAAGTTAACTTCCAA 58.215 29.630 20.78 16.74 34.61 3.53
353 356 9.058424 GCGATTGTTATAAAGTTAACTTCCAAC 57.942 33.333 20.78 21.12 34.61 3.77
354 357 9.550811 CGATTGTTATAAAGTTAACTTCCAACC 57.449 33.333 20.78 10.04 34.61 3.77
355 358 9.550811 GATTGTTATAAAGTTAACTTCCAACCG 57.449 33.333 20.78 0.00 34.61 4.44
356 359 8.674263 TTGTTATAAAGTTAACTTCCAACCGA 57.326 30.769 20.78 12.44 34.61 4.69
357 360 8.674263 TGTTATAAAGTTAACTTCCAACCGAA 57.326 30.769 20.78 7.43 34.61 4.30
358 361 9.118300 TGTTATAAAGTTAACTTCCAACCGAAA 57.882 29.630 20.78 7.14 34.61 3.46
359 362 9.385902 GTTATAAAGTTAACTTCCAACCGAAAC 57.614 33.333 20.78 12.26 34.61 2.78
360 363 4.906065 AAGTTAACTTCCAACCGAAACC 57.094 40.909 15.22 0.00 0.00 3.27
361 364 2.874086 AGTTAACTTCCAACCGAAACCG 59.126 45.455 1.12 0.00 0.00 4.44
362 365 2.613595 GTTAACTTCCAACCGAAACCGT 59.386 45.455 0.00 0.00 0.00 4.83
363 366 1.753930 AACTTCCAACCGAAACCGTT 58.246 45.000 0.00 0.00 0.00 4.44
364 367 1.753930 ACTTCCAACCGAAACCGTTT 58.246 45.000 0.00 0.00 0.00 3.60
365 368 1.672363 ACTTCCAACCGAAACCGTTTC 59.328 47.619 13.16 13.16 36.32 2.78
366 369 1.002142 CTTCCAACCGAAACCGTTTCC 60.002 52.381 16.61 1.87 36.30 3.13
367 370 1.159098 TCCAACCGAAACCGTTTCCG 61.159 55.000 16.61 13.08 36.30 4.30
368 371 1.159098 CCAACCGAAACCGTTTCCGA 61.159 55.000 16.61 0.00 36.30 4.55
369 372 0.656785 CAACCGAAACCGTTTCCGAA 59.343 50.000 16.61 0.00 36.30 4.30
370 373 1.264826 CAACCGAAACCGTTTCCGAAT 59.735 47.619 16.61 4.63 36.30 3.34
371 374 1.150827 ACCGAAACCGTTTCCGAATC 58.849 50.000 16.61 0.00 36.30 2.52
372 375 0.445043 CCGAAACCGTTTCCGAATCC 59.555 55.000 16.61 0.00 36.30 3.01
373 376 1.149987 CGAAACCGTTTCCGAATCCA 58.850 50.000 16.61 0.00 36.30 3.41
374 377 1.735571 CGAAACCGTTTCCGAATCCAT 59.264 47.619 16.61 0.00 36.30 3.41
375 378 2.160813 CGAAACCGTTTCCGAATCCATT 59.839 45.455 16.61 0.00 36.30 3.16
376 379 3.365565 CGAAACCGTTTCCGAATCCATTT 60.366 43.478 16.61 0.00 36.30 2.32
377 380 4.552355 GAAACCGTTTCCGAATCCATTTT 58.448 39.130 12.28 0.00 35.63 1.82
378 381 5.617308 CGAAACCGTTTCCGAATCCATTTTA 60.617 40.000 16.61 0.00 36.30 1.52
379 382 5.708877 AACCGTTTCCGAATCCATTTTAA 57.291 34.783 0.00 0.00 35.63 1.52
380 383 5.907866 ACCGTTTCCGAATCCATTTTAAT 57.092 34.783 0.00 0.00 35.63 1.40
381 384 7.393841 AACCGTTTCCGAATCCATTTTAATA 57.606 32.000 0.00 0.00 35.63 0.98
382 385 7.576861 ACCGTTTCCGAATCCATTTTAATAT 57.423 32.000 0.00 0.00 35.63 1.28
383 386 7.422399 ACCGTTTCCGAATCCATTTTAATATG 58.578 34.615 0.00 0.00 35.63 1.78
384 387 6.861055 CCGTTTCCGAATCCATTTTAATATGG 59.139 38.462 16.46 16.46 40.59 2.74
385 388 7.422399 CGTTTCCGAATCCATTTTAATATGGT 58.578 34.615 20.33 6.35 40.33 3.55
386 389 8.561212 CGTTTCCGAATCCATTTTAATATGGTA 58.439 33.333 20.33 10.64 40.33 3.25
387 390 9.673454 GTTTCCGAATCCATTTTAATATGGTAC 57.327 33.333 20.33 13.27 44.48 3.34
388 391 7.989416 TCCGAATCCATTTTAATATGGTACC 57.011 36.000 20.33 4.43 44.48 3.34
389 392 7.519057 TCCGAATCCATTTTAATATGGTACCA 58.481 34.615 18.99 18.99 44.48 3.25
390 393 8.167392 TCCGAATCCATTTTAATATGGTACCAT 58.833 33.333 29.68 29.68 44.48 3.55
391 394 9.456147 CCGAATCCATTTTAATATGGTACCATA 57.544 33.333 31.81 31.81 44.48 2.74
408 411 9.793259 TGGTACCATAAGATATTTTTGAGATCC 57.207 33.333 11.60 0.00 0.00 3.36
409 412 9.793259 GGTACCATAAGATATTTTTGAGATCCA 57.207 33.333 7.15 0.00 0.00 3.41
419 422 9.305925 GATATTTTTGAGATCCAAACACAATCC 57.694 33.333 8.36 1.89 43.82 3.01
420 423 5.467035 TTTTGAGATCCAAACACAATCCC 57.533 39.130 8.36 0.00 43.82 3.85
421 424 2.710377 TGAGATCCAAACACAATCCCG 58.290 47.619 0.00 0.00 0.00 5.14
422 425 2.304470 TGAGATCCAAACACAATCCCGA 59.696 45.455 0.00 0.00 0.00 5.14
423 426 2.939103 GAGATCCAAACACAATCCCGAG 59.061 50.000 0.00 0.00 0.00 4.63
424 427 2.305927 AGATCCAAACACAATCCCGAGT 59.694 45.455 0.00 0.00 0.00 4.18
425 428 2.178912 TCCAAACACAATCCCGAGTC 57.821 50.000 0.00 0.00 0.00 3.36
426 429 1.165270 CCAAACACAATCCCGAGTCC 58.835 55.000 0.00 0.00 0.00 3.85
427 430 1.544537 CCAAACACAATCCCGAGTCCA 60.545 52.381 0.00 0.00 0.00 4.02
428 431 2.226330 CAAACACAATCCCGAGTCCAA 58.774 47.619 0.00 0.00 0.00 3.53
429 432 1.892209 AACACAATCCCGAGTCCAAC 58.108 50.000 0.00 0.00 0.00 3.77
430 433 1.056660 ACACAATCCCGAGTCCAACT 58.943 50.000 0.00 0.00 0.00 3.16
431 434 1.270839 ACACAATCCCGAGTCCAACTG 60.271 52.381 0.00 0.00 0.00 3.16
432 435 1.056660 ACAATCCCGAGTCCAACTGT 58.943 50.000 0.00 0.00 0.00 3.55
433 436 1.270839 ACAATCCCGAGTCCAACTGTG 60.271 52.381 0.00 0.00 0.00 3.66
434 437 1.056660 AATCCCGAGTCCAACTGTGT 58.943 50.000 0.00 0.00 0.00 3.72
435 438 1.933021 ATCCCGAGTCCAACTGTGTA 58.067 50.000 0.00 0.00 0.00 2.90
436 439 1.933021 TCCCGAGTCCAACTGTGTAT 58.067 50.000 0.00 0.00 0.00 2.29
437 440 3.090210 TCCCGAGTCCAACTGTGTATA 57.910 47.619 0.00 0.00 0.00 1.47
438 441 3.021695 TCCCGAGTCCAACTGTGTATAG 58.978 50.000 0.00 0.00 0.00 1.31
439 442 2.100916 CCCGAGTCCAACTGTGTATAGG 59.899 54.545 0.00 0.00 0.00 2.57
440 443 3.021695 CCGAGTCCAACTGTGTATAGGA 58.978 50.000 0.00 0.00 0.00 2.94
441 444 3.637229 CCGAGTCCAACTGTGTATAGGAT 59.363 47.826 0.00 0.00 0.00 3.24
442 445 4.825634 CCGAGTCCAACTGTGTATAGGATA 59.174 45.833 0.00 0.00 0.00 2.59
443 446 5.477291 CCGAGTCCAACTGTGTATAGGATAT 59.523 44.000 0.00 0.00 0.00 1.63
444 447 6.657966 CCGAGTCCAACTGTGTATAGGATATA 59.342 42.308 0.00 0.00 0.00 0.86
445 448 7.148222 CCGAGTCCAACTGTGTATAGGATATAG 60.148 44.444 0.00 0.00 0.00 1.31
446 449 7.606839 CGAGTCCAACTGTGTATAGGATATAGA 59.393 40.741 0.00 0.00 0.00 1.98
447 450 8.638629 AGTCCAACTGTGTATAGGATATAGAC 57.361 38.462 0.00 0.00 0.00 2.59
448 451 7.390996 AGTCCAACTGTGTATAGGATATAGACG 59.609 40.741 0.00 0.00 0.00 4.18
449 452 7.389884 GTCCAACTGTGTATAGGATATAGACGA 59.610 40.741 0.00 0.00 0.00 4.20
450 453 7.389884 TCCAACTGTGTATAGGATATAGACGAC 59.610 40.741 0.00 0.00 0.00 4.34
451 454 7.174426 CCAACTGTGTATAGGATATAGACGACA 59.826 40.741 0.00 0.00 0.00 4.35
452 455 7.670009 ACTGTGTATAGGATATAGACGACAC 57.330 40.000 0.00 0.00 37.15 3.67
453 456 6.654161 ACTGTGTATAGGATATAGACGACACC 59.346 42.308 0.00 0.00 36.06 4.16
454 457 5.640783 TGTGTATAGGATATAGACGACACCG 59.359 44.000 0.00 0.00 42.50 4.94
473 476 3.955650 CGTAGGAATGGATAATCCGGT 57.044 47.619 0.00 0.00 40.17 5.28
474 477 4.267349 CGTAGGAATGGATAATCCGGTT 57.733 45.455 0.00 0.00 40.17 4.44
475 478 4.638304 CGTAGGAATGGATAATCCGGTTT 58.362 43.478 0.00 1.12 40.17 3.27
476 479 5.061179 CGTAGGAATGGATAATCCGGTTTT 58.939 41.667 0.00 0.00 40.17 2.43
477 480 5.529800 CGTAGGAATGGATAATCCGGTTTTT 59.470 40.000 0.00 0.00 40.17 1.94
478 481 6.293244 CGTAGGAATGGATAATCCGGTTTTTC 60.293 42.308 0.00 4.13 40.17 2.29
479 482 5.766590 AGGAATGGATAATCCGGTTTTTCT 58.233 37.500 13.29 0.00 40.17 2.52
480 483 6.906848 AGGAATGGATAATCCGGTTTTTCTA 58.093 36.000 13.29 9.19 40.17 2.10
481 484 6.998673 AGGAATGGATAATCCGGTTTTTCTAG 59.001 38.462 13.29 0.00 40.17 2.43
482 485 6.294010 GGAATGGATAATCCGGTTTTTCTAGC 60.294 42.308 13.29 6.13 40.17 3.42
483 486 4.457466 TGGATAATCCGGTTTTTCTAGCC 58.543 43.478 13.29 4.82 40.17 3.93
484 487 3.497262 GGATAATCCGGTTTTTCTAGCCG 59.503 47.826 13.29 0.00 44.55 5.52
491 494 4.727235 CGGTTTTTCTAGCCGGATAATC 57.273 45.455 5.05 0.00 41.60 1.75
492 495 4.377897 CGGTTTTTCTAGCCGGATAATCT 58.622 43.478 5.05 0.00 41.60 2.40
493 496 4.211374 CGGTTTTTCTAGCCGGATAATCTG 59.789 45.833 5.05 0.00 41.60 2.90
494 497 5.365619 GGTTTTTCTAGCCGGATAATCTGA 58.634 41.667 5.05 0.00 0.00 3.27
495 498 5.998363 GGTTTTTCTAGCCGGATAATCTGAT 59.002 40.000 5.05 0.00 0.00 2.90
496 499 6.147985 GGTTTTTCTAGCCGGATAATCTGATC 59.852 42.308 5.05 0.00 0.00 2.92
497 500 5.407407 TTTCTAGCCGGATAATCTGATCC 57.593 43.478 5.05 0.00 41.89 3.36
498 501 4.323569 TCTAGCCGGATAATCTGATCCT 57.676 45.455 5.05 0.00 42.97 3.24
499 502 4.678256 TCTAGCCGGATAATCTGATCCTT 58.322 43.478 5.05 0.00 42.97 3.36
500 503 3.971245 AGCCGGATAATCTGATCCTTC 57.029 47.619 5.05 0.00 42.97 3.46
501 504 3.242867 AGCCGGATAATCTGATCCTTCA 58.757 45.455 5.05 0.00 42.97 3.02
502 505 3.648067 AGCCGGATAATCTGATCCTTCAA 59.352 43.478 5.05 0.00 42.97 2.69
503 506 4.103153 AGCCGGATAATCTGATCCTTCAAA 59.897 41.667 5.05 0.00 42.97 2.69
504 507 4.821805 GCCGGATAATCTGATCCTTCAAAA 59.178 41.667 5.05 0.00 42.97 2.44
505 508 5.299279 GCCGGATAATCTGATCCTTCAAAAA 59.701 40.000 5.05 0.00 42.97 1.94
541 544 5.493133 ACGCTTTATGTGTGAAGTTTGAA 57.507 34.783 0.00 0.00 38.09 2.69
542 545 5.510671 ACGCTTTATGTGTGAAGTTTGAAG 58.489 37.500 0.00 0.00 38.09 3.02
543 546 5.065988 ACGCTTTATGTGTGAAGTTTGAAGT 59.934 36.000 0.00 0.00 38.09 3.01
544 547 6.259167 ACGCTTTATGTGTGAAGTTTGAAGTA 59.741 34.615 0.00 0.00 38.09 2.24
545 548 7.041372 ACGCTTTATGTGTGAAGTTTGAAGTAT 60.041 33.333 0.00 0.00 38.09 2.12
546 549 7.803189 CGCTTTATGTGTGAAGTTTGAAGTATT 59.197 33.333 0.00 0.00 0.00 1.89
553 556 8.770828 TGTGTGAAGTTTGAAGTATTAACTAGC 58.229 33.333 0.00 0.00 33.75 3.42
554 557 8.770828 GTGTGAAGTTTGAAGTATTAACTAGCA 58.229 33.333 0.00 0.00 33.75 3.49
555 558 9.332502 TGTGAAGTTTGAAGTATTAACTAGCAA 57.667 29.630 0.00 0.00 33.75 3.91
558 561 9.331106 GAAGTTTGAAGTATTAACTAGCAAAGC 57.669 33.333 0.00 0.00 39.13 3.51
559 562 8.622948 AGTTTGAAGTATTAACTAGCAAAGCT 57.377 30.769 0.00 0.00 39.13 3.74
560 563 9.067986 AGTTTGAAGTATTAACTAGCAAAGCTT 57.932 29.630 0.00 0.00 39.13 3.74
561 564 9.118236 GTTTGAAGTATTAACTAGCAAAGCTTG 57.882 33.333 0.00 0.00 39.13 4.01
562 565 8.615878 TTGAAGTATTAACTAGCAAAGCTTGA 57.384 30.769 0.00 0.00 40.44 3.02
563 566 8.256611 TGAAGTATTAACTAGCAAAGCTTGAG 57.743 34.615 0.00 0.00 40.44 3.02
564 567 7.878127 TGAAGTATTAACTAGCAAAGCTTGAGT 59.122 33.333 0.00 0.00 40.44 3.41
565 568 7.602517 AGTATTAACTAGCAAAGCTTGAGTG 57.397 36.000 0.00 0.00 40.44 3.51
566 569 4.749245 TTAACTAGCAAAGCTTGAGTGC 57.251 40.909 12.71 12.71 40.44 4.40
568 571 3.685139 ACTAGCAAAGCTTGAGTGCTA 57.315 42.857 23.36 23.36 46.52 3.49
569 572 4.213564 ACTAGCAAAGCTTGAGTGCTAT 57.786 40.909 24.48 15.23 46.70 2.97
570 573 4.187694 ACTAGCAAAGCTTGAGTGCTATC 58.812 43.478 24.48 0.00 46.70 2.08
571 574 3.347077 AGCAAAGCTTGAGTGCTATCT 57.653 42.857 19.98 0.00 46.52 1.98
572 575 3.683802 AGCAAAGCTTGAGTGCTATCTT 58.316 40.909 19.98 0.00 46.52 2.40
573 576 4.077822 AGCAAAGCTTGAGTGCTATCTTT 58.922 39.130 19.98 0.00 46.52 2.52
574 577 4.082895 AGCAAAGCTTGAGTGCTATCTTTG 60.083 41.667 19.98 2.31 46.52 2.77
575 578 4.164294 CAAAGCTTGAGTGCTATCTTTGC 58.836 43.478 0.00 0.00 43.24 3.68
576 579 3.347077 AGCTTGAGTGCTATCTTTGCT 57.653 42.857 0.00 0.00 42.10 3.91
577 580 3.683802 AGCTTGAGTGCTATCTTTGCTT 58.316 40.909 0.00 0.00 42.10 3.91
578 581 3.439476 AGCTTGAGTGCTATCTTTGCTTG 59.561 43.478 0.00 0.00 42.10 4.01
579 582 3.190118 GCTTGAGTGCTATCTTTGCTTGT 59.810 43.478 0.00 0.00 0.00 3.16
580 583 4.720090 CTTGAGTGCTATCTTTGCTTGTG 58.280 43.478 0.00 0.00 0.00 3.33
581 584 4.006780 TGAGTGCTATCTTTGCTTGTGA 57.993 40.909 0.00 0.00 0.00 3.58
582 585 3.999001 TGAGTGCTATCTTTGCTTGTGAG 59.001 43.478 0.00 0.00 0.00 3.51
583 586 4.248859 GAGTGCTATCTTTGCTTGTGAGA 58.751 43.478 0.00 0.00 0.00 3.27
584 587 4.252073 AGTGCTATCTTTGCTTGTGAGAG 58.748 43.478 0.00 0.00 0.00 3.20
585 588 4.020751 AGTGCTATCTTTGCTTGTGAGAGA 60.021 41.667 0.00 0.00 0.00 3.10
586 589 4.692625 GTGCTATCTTTGCTTGTGAGAGAA 59.307 41.667 0.00 0.00 0.00 2.87
587 590 5.180117 GTGCTATCTTTGCTTGTGAGAGAAA 59.820 40.000 0.00 0.00 0.00 2.52
588 591 5.764686 TGCTATCTTTGCTTGTGAGAGAAAA 59.235 36.000 0.00 0.00 0.00 2.29
589 592 6.082984 GCTATCTTTGCTTGTGAGAGAAAAC 58.917 40.000 0.00 0.00 0.00 2.43
590 593 4.536364 TCTTTGCTTGTGAGAGAAAACG 57.464 40.909 0.00 0.00 0.00 3.60
591 594 3.938963 TCTTTGCTTGTGAGAGAAAACGT 59.061 39.130 0.00 0.00 0.00 3.99
592 595 5.113383 TCTTTGCTTGTGAGAGAAAACGTA 58.887 37.500 0.00 0.00 0.00 3.57
593 596 5.583061 TCTTTGCTTGTGAGAGAAAACGTAA 59.417 36.000 0.00 0.00 0.00 3.18
623 626 9.649167 AATTTGTGTACTACTAATGTACCTGAC 57.351 33.333 0.00 0.00 39.42 3.51
624 627 8.413309 TTTGTGTACTACTAATGTACCTGACT 57.587 34.615 0.00 0.00 39.42 3.41
625 628 8.413309 TTGTGTACTACTAATGTACCTGACTT 57.587 34.615 0.00 0.00 39.42 3.01
626 629 8.413309 TGTGTACTACTAATGTACCTGACTTT 57.587 34.615 0.00 0.00 39.42 2.66
627 630 8.517878 TGTGTACTACTAATGTACCTGACTTTC 58.482 37.037 0.00 0.00 39.42 2.62
628 631 7.972832 GTGTACTACTAATGTACCTGACTTTCC 59.027 40.741 0.00 0.00 39.42 3.13
629 632 7.670979 TGTACTACTAATGTACCTGACTTTCCA 59.329 37.037 0.00 0.00 39.42 3.53
630 633 7.171630 ACTACTAATGTACCTGACTTTCCAG 57.828 40.000 0.00 0.00 0.00 3.86
631 634 6.724905 ACTACTAATGTACCTGACTTTCCAGT 59.275 38.462 0.00 0.00 35.17 4.00
632 635 5.794894 ACTAATGTACCTGACTTTCCAGTG 58.205 41.667 0.00 0.00 31.22 3.66
633 636 2.543777 TGTACCTGACTTTCCAGTGC 57.456 50.000 0.00 0.00 31.22 4.40
634 637 2.047061 TGTACCTGACTTTCCAGTGCT 58.953 47.619 0.00 0.00 31.22 4.40
635 638 2.438021 TGTACCTGACTTTCCAGTGCTT 59.562 45.455 0.00 0.00 31.22 3.91
636 639 2.736670 ACCTGACTTTCCAGTGCTTT 57.263 45.000 0.00 0.00 31.22 3.51
637 640 2.301346 ACCTGACTTTCCAGTGCTTTG 58.699 47.619 0.00 0.00 31.22 2.77
638 641 2.301346 CCTGACTTTCCAGTGCTTTGT 58.699 47.619 0.00 0.00 31.22 2.83
639 642 2.033801 CCTGACTTTCCAGTGCTTTGTG 59.966 50.000 0.00 0.00 31.22 3.33
640 643 2.684881 CTGACTTTCCAGTGCTTTGTGT 59.315 45.455 0.00 0.00 31.22 3.72
641 644 3.876914 CTGACTTTCCAGTGCTTTGTGTA 59.123 43.478 0.00 0.00 31.22 2.90
642 645 4.460263 TGACTTTCCAGTGCTTTGTGTAT 58.540 39.130 0.00 0.00 31.22 2.29
643 646 4.275689 TGACTTTCCAGTGCTTTGTGTATG 59.724 41.667 0.00 0.00 31.22 2.39
644 647 4.207165 ACTTTCCAGTGCTTTGTGTATGT 58.793 39.130 0.00 0.00 0.00 2.29
645 648 4.644685 ACTTTCCAGTGCTTTGTGTATGTT 59.355 37.500 0.00 0.00 0.00 2.71
646 649 5.127031 ACTTTCCAGTGCTTTGTGTATGTTT 59.873 36.000 0.00 0.00 0.00 2.83
647 650 6.320164 ACTTTCCAGTGCTTTGTGTATGTTTA 59.680 34.615 0.00 0.00 0.00 2.01
648 651 6.701145 TTCCAGTGCTTTGTGTATGTTTAA 57.299 33.333 0.00 0.00 0.00 1.52
649 652 6.701145 TCCAGTGCTTTGTGTATGTTTAAA 57.299 33.333 0.00 0.00 0.00 1.52
650 653 6.734137 TCCAGTGCTTTGTGTATGTTTAAAG 58.266 36.000 0.00 0.00 34.22 1.85
651 654 6.320164 TCCAGTGCTTTGTGTATGTTTAAAGT 59.680 34.615 0.00 0.00 33.76 2.66
652 655 6.417635 CCAGTGCTTTGTGTATGTTTAAAGTG 59.582 38.462 0.00 0.00 33.76 3.16
653 656 6.972328 CAGTGCTTTGTGTATGTTTAAAGTGT 59.028 34.615 0.00 0.00 33.76 3.55
654 657 8.126074 CAGTGCTTTGTGTATGTTTAAAGTGTA 58.874 33.333 0.00 0.00 33.76 2.90
655 658 8.126700 AGTGCTTTGTGTATGTTTAAAGTGTAC 58.873 33.333 0.00 0.00 33.76 2.90
656 659 7.911205 GTGCTTTGTGTATGTTTAAAGTGTACA 59.089 33.333 0.00 0.00 33.76 2.90
657 660 8.459635 TGCTTTGTGTATGTTTAAAGTGTACAA 58.540 29.630 0.00 5.39 33.76 2.41
658 661 8.953990 GCTTTGTGTATGTTTAAAGTGTACAAG 58.046 33.333 0.00 5.35 33.76 3.16
659 662 9.997482 CTTTGTGTATGTTTAAAGTGTACAAGT 57.003 29.630 0.00 0.00 0.00 3.16
703 706 7.022055 TGTATTTACATATTCGGTTGGCTTG 57.978 36.000 0.00 0.00 0.00 4.01
704 707 6.824196 TGTATTTACATATTCGGTTGGCTTGA 59.176 34.615 0.00 0.00 0.00 3.02
705 708 5.811399 TTTACATATTCGGTTGGCTTGAG 57.189 39.130 0.00 0.00 0.00 3.02
706 709 3.627395 ACATATTCGGTTGGCTTGAGA 57.373 42.857 0.00 0.00 0.00 3.27
707 710 3.535561 ACATATTCGGTTGGCTTGAGAG 58.464 45.455 0.00 0.00 0.00 3.20
825 841 7.331026 CACTAGATGAAATGGGTTAGAACAGA 58.669 38.462 0.00 0.00 0.00 3.41
892 908 0.106719 TTCCTCGCCAATCCCCATTC 60.107 55.000 0.00 0.00 0.00 2.67
893 909 1.227102 CCTCGCCAATCCCCATTCA 59.773 57.895 0.00 0.00 0.00 2.57
894 910 1.103398 CCTCGCCAATCCCCATTCAC 61.103 60.000 0.00 0.00 0.00 3.18
936 953 4.408821 CTAGCTGCGCCAACCCCA 62.409 66.667 4.18 0.00 0.00 4.96
937 954 3.918253 CTAGCTGCGCCAACCCCAA 62.918 63.158 4.18 0.00 0.00 4.12
1246 1292 2.048222 TGTTTCTCCAGGCGCTCG 60.048 61.111 7.64 0.00 0.00 5.03
1356 1411 1.270358 GCTGTATCTGGATCCGGTTCC 60.270 57.143 22.64 22.64 36.24 3.62
1373 3788 3.055312 GGTTCCGAGTTCCAGAAGGTATT 60.055 47.826 0.00 0.00 35.89 1.89
1451 5011 2.702478 TGGCTGAGCTCTGCACTAATAT 59.298 45.455 36.57 0.00 41.76 1.28
1500 5079 6.373005 TTCTAATCAAGTTGTCCTGATGGA 57.627 37.500 2.11 0.00 40.69 3.41
1515 5095 7.018449 TGTCCTGATGGAAATATGAATGGGATA 59.982 37.037 0.00 0.00 45.18 2.59
1564 5144 1.854126 GCATCATTCAATTTTCGGCCG 59.146 47.619 22.12 22.12 0.00 6.13
1582 5162 2.677199 CCGATTCCATACTCATGTCCG 58.323 52.381 0.00 0.00 0.00 4.79
1606 5186 3.862267 CGTTGTGGTTTTGCTGAATTTGA 59.138 39.130 0.00 0.00 0.00 2.69
1693 5273 1.301479 AGTCCTTGGAACGTTCGCC 60.301 57.895 21.34 10.52 0.00 5.54
2031 5611 7.685304 GTGAATTTGCAATCATTTTTCTTAGCG 59.315 33.333 0.00 0.00 0.00 4.26
2033 5613 3.510719 TGCAATCATTTTTCTTAGCGGC 58.489 40.909 0.00 0.00 0.00 6.53
2273 5856 8.196378 AGTACTGATCTTCTTTGGTTAAGTCT 57.804 34.615 0.00 0.00 35.28 3.24
2299 5882 5.894298 ATTGACCAATCAGATGCCTACTA 57.106 39.130 0.00 0.00 35.83 1.82
2348 5931 3.435327 GCGTTGTTCATGTCCAGTCATTA 59.565 43.478 0.00 0.00 0.00 1.90
2369 5952 2.158325 ACTGGGATTGTTGTGATTGGGT 60.158 45.455 0.00 0.00 0.00 4.51
2384 5967 8.076910 TGTGATTGGGTAGCAATTTATTCATT 57.923 30.769 0.00 0.00 0.00 2.57
2439 6022 4.740822 GGCTGGGTTGTCGGGCAT 62.741 66.667 0.00 0.00 38.32 4.40
2441 6024 2.671070 CTGGGTTGTCGGGCATCT 59.329 61.111 0.00 0.00 0.00 2.90
2498 6081 5.533154 TCCGCCTTGTTTTATATGTTATGGG 59.467 40.000 0.00 0.00 0.00 4.00
2544 6127 6.817641 AGTGAAGATAGCAAACAGAATCTCAG 59.182 38.462 0.00 0.00 0.00 3.35
2570 6176 4.060038 ACTATTCAAGTCGGTAGCATGG 57.940 45.455 0.00 0.00 30.33 3.66
2635 6241 3.820557 ACTTTCTACTTGCATGTGGTGT 58.179 40.909 15.08 9.89 0.00 4.16
2636 6242 4.207165 ACTTTCTACTTGCATGTGGTGTT 58.793 39.130 15.08 0.00 0.00 3.32
2637 6243 5.373222 ACTTTCTACTTGCATGTGGTGTTA 58.627 37.500 15.08 0.00 0.00 2.41
2664 6270 7.482169 ACTCCATGTCATTTCTGTAGAAGTA 57.518 36.000 0.00 0.00 35.21 2.24
2707 6313 6.103997 TGACGTTGTAGTGAAATATTCTCCC 58.896 40.000 0.00 0.00 0.00 4.30
2725 6331 2.622962 CCTTTCACGGGGTTTCGGC 61.623 63.158 0.00 0.00 0.00 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 6.775629 TGATTTTACTGTTAGCTGGGAACTTT 59.224 34.615 0.00 0.00 0.00 2.66
37 38 9.855021 ACAAATATGGTTGATTTTACTGTTAGC 57.145 29.630 0.00 0.00 32.59 3.09
73 74 3.563508 TGCATATCAAAACTGTTGTGCG 58.436 40.909 5.82 0.00 34.28 5.34
125 127 4.231439 GTTTTTCAAGTTGACAACACCGT 58.769 39.130 20.08 0.00 0.00 4.83
247 250 7.775053 TTGTTAGCCCATAGAAACTCAAATT 57.225 32.000 0.00 0.00 0.00 1.82
255 258 7.990886 AGTATTCGAATTGTTAGCCCATAGAAA 59.009 33.333 17.19 0.00 0.00 2.52
256 259 7.506114 AGTATTCGAATTGTTAGCCCATAGAA 58.494 34.615 17.19 0.00 0.00 2.10
329 332 9.550811 CGGTTGGAAGTTAACTTTATAACAATC 57.449 33.333 26.59 21.39 38.07 2.67
333 336 9.385902 GTTTCGGTTGGAAGTTAACTTTATAAC 57.614 33.333 21.40 21.86 36.11 1.89
335 338 7.095271 CGGTTTCGGTTGGAAGTTAACTTTATA 60.095 37.037 21.40 8.80 36.11 0.98
336 339 6.293571 CGGTTTCGGTTGGAAGTTAACTTTAT 60.294 38.462 21.40 0.00 36.11 1.40
337 340 5.007528 CGGTTTCGGTTGGAAGTTAACTTTA 59.992 40.000 21.40 11.47 36.11 1.85
338 341 4.201940 CGGTTTCGGTTGGAAGTTAACTTT 60.202 41.667 21.40 6.19 36.11 2.66
339 342 3.313249 CGGTTTCGGTTGGAAGTTAACTT 59.687 43.478 20.67 20.67 39.23 2.66
340 343 2.874086 CGGTTTCGGTTGGAAGTTAACT 59.126 45.455 1.12 1.12 35.70 2.24
341 344 2.613595 ACGGTTTCGGTTGGAAGTTAAC 59.386 45.455 0.00 0.00 41.39 2.01
342 345 2.916640 ACGGTTTCGGTTGGAAGTTAA 58.083 42.857 0.00 0.00 41.39 2.01
343 346 2.618442 ACGGTTTCGGTTGGAAGTTA 57.382 45.000 0.00 0.00 41.39 2.24
344 347 1.753930 AACGGTTTCGGTTGGAAGTT 58.246 45.000 0.00 0.00 41.39 2.66
345 348 1.753930 AAACGGTTTCGGTTGGAAGT 58.246 45.000 0.00 0.00 45.50 3.01
382 385 9.793259 GGATCTCAAAAATATCTTATGGTACCA 57.207 33.333 18.99 18.99 0.00 3.25
383 386 9.793259 TGGATCTCAAAAATATCTTATGGTACC 57.207 33.333 4.43 4.43 0.00 3.34
393 396 9.305925 GGATTGTGTTTGGATCTCAAAAATATC 57.694 33.333 9.91 10.85 45.74 1.63
394 397 8.260114 GGGATTGTGTTTGGATCTCAAAAATAT 58.740 33.333 9.91 4.88 45.74 1.28
395 398 7.576666 CGGGATTGTGTTTGGATCTCAAAAATA 60.577 37.037 9.91 2.77 45.74 1.40
396 399 6.466812 GGGATTGTGTTTGGATCTCAAAAAT 58.533 36.000 9.91 7.45 45.74 1.82
397 400 5.508825 CGGGATTGTGTTTGGATCTCAAAAA 60.509 40.000 9.91 3.91 45.74 1.94
398 401 4.022416 CGGGATTGTGTTTGGATCTCAAAA 60.022 41.667 9.91 0.00 45.74 2.44
399 402 3.505680 CGGGATTGTGTTTGGATCTCAAA 59.494 43.478 5.55 5.55 42.50 2.69
400 403 3.081061 CGGGATTGTGTTTGGATCTCAA 58.919 45.455 0.00 0.00 0.00 3.02
401 404 2.304470 TCGGGATTGTGTTTGGATCTCA 59.696 45.455 0.00 0.00 0.00 3.27
402 405 2.939103 CTCGGGATTGTGTTTGGATCTC 59.061 50.000 0.00 0.00 0.00 2.75
403 406 2.305927 ACTCGGGATTGTGTTTGGATCT 59.694 45.455 0.00 0.00 0.00 2.75
404 407 2.678336 GACTCGGGATTGTGTTTGGATC 59.322 50.000 0.00 0.00 0.00 3.36
405 408 2.618045 GGACTCGGGATTGTGTTTGGAT 60.618 50.000 0.00 0.00 0.00 3.41
406 409 1.271163 GGACTCGGGATTGTGTTTGGA 60.271 52.381 0.00 0.00 0.00 3.53
407 410 1.165270 GGACTCGGGATTGTGTTTGG 58.835 55.000 0.00 0.00 0.00 3.28
408 411 1.890876 TGGACTCGGGATTGTGTTTG 58.109 50.000 0.00 0.00 0.00 2.93
409 412 2.158667 AGTTGGACTCGGGATTGTGTTT 60.159 45.455 0.00 0.00 0.00 2.83
410 413 1.420138 AGTTGGACTCGGGATTGTGTT 59.580 47.619 0.00 0.00 0.00 3.32
411 414 1.056660 AGTTGGACTCGGGATTGTGT 58.943 50.000 0.00 0.00 0.00 3.72
412 415 1.270839 ACAGTTGGACTCGGGATTGTG 60.271 52.381 0.00 0.00 0.00 3.33
413 416 1.056660 ACAGTTGGACTCGGGATTGT 58.943 50.000 0.00 0.00 0.00 2.71
414 417 1.270839 ACACAGTTGGACTCGGGATTG 60.271 52.381 0.00 0.00 0.00 2.67
415 418 1.056660 ACACAGTTGGACTCGGGATT 58.943 50.000 0.00 0.00 0.00 3.01
416 419 1.933021 TACACAGTTGGACTCGGGAT 58.067 50.000 0.00 0.00 0.00 3.85
417 420 1.933021 ATACACAGTTGGACTCGGGA 58.067 50.000 0.00 0.00 0.00 5.14
418 421 2.100916 CCTATACACAGTTGGACTCGGG 59.899 54.545 0.00 0.00 0.00 5.14
419 422 3.021695 TCCTATACACAGTTGGACTCGG 58.978 50.000 0.00 0.00 0.00 4.63
420 423 4.920640 ATCCTATACACAGTTGGACTCG 57.079 45.455 0.00 0.00 0.00 4.18
421 424 8.732531 GTCTATATCCTATACACAGTTGGACTC 58.267 40.741 0.00 0.00 0.00 3.36
422 425 7.390996 CGTCTATATCCTATACACAGTTGGACT 59.609 40.741 0.00 0.00 0.00 3.85
423 426 7.389884 TCGTCTATATCCTATACACAGTTGGAC 59.610 40.741 0.00 0.00 0.00 4.02
424 427 7.389884 GTCGTCTATATCCTATACACAGTTGGA 59.610 40.741 0.00 0.00 0.00 3.53
425 428 7.174426 TGTCGTCTATATCCTATACACAGTTGG 59.826 40.741 0.00 0.00 0.00 3.77
426 429 8.016229 GTGTCGTCTATATCCTATACACAGTTG 58.984 40.741 0.00 0.00 36.77 3.16
427 430 7.174599 GGTGTCGTCTATATCCTATACACAGTT 59.825 40.741 0.00 0.00 38.13 3.16
428 431 6.654161 GGTGTCGTCTATATCCTATACACAGT 59.346 42.308 0.00 0.00 38.13 3.55
429 432 6.183360 CGGTGTCGTCTATATCCTATACACAG 60.183 46.154 0.00 0.00 38.13 3.66
430 433 5.640783 CGGTGTCGTCTATATCCTATACACA 59.359 44.000 0.00 0.00 38.13 3.72
431 434 6.104439 CGGTGTCGTCTATATCCTATACAC 57.896 45.833 0.00 0.00 36.20 2.90
445 448 8.926393 GGATTATCCATTCCTACGGTGTCGTC 62.926 50.000 6.34 0.00 41.96 4.20
446 449 7.240270 GGATTATCCATTCCTACGGTGTCGT 62.240 48.000 6.34 0.00 43.85 4.34
447 450 3.720949 TTATCCATTCCTACGGTGTCG 57.279 47.619 0.00 0.00 43.02 4.35
448 451 4.566987 GGATTATCCATTCCTACGGTGTC 58.433 47.826 6.34 0.00 36.28 3.67
449 452 3.006537 CGGATTATCCATTCCTACGGTGT 59.993 47.826 12.17 0.00 35.91 4.16
450 453 3.585862 CGGATTATCCATTCCTACGGTG 58.414 50.000 12.17 0.00 35.91 4.94
451 454 2.565834 CCGGATTATCCATTCCTACGGT 59.434 50.000 12.17 0.00 35.91 4.83
452 455 2.565834 ACCGGATTATCCATTCCTACGG 59.434 50.000 9.46 6.41 43.93 4.02
453 456 3.955650 ACCGGATTATCCATTCCTACG 57.044 47.619 9.46 0.00 35.91 3.51
454 457 6.771267 AGAAAAACCGGATTATCCATTCCTAC 59.229 38.462 9.46 0.00 35.91 3.18
455 458 6.906848 AGAAAAACCGGATTATCCATTCCTA 58.093 36.000 9.46 0.00 35.91 2.94
456 459 5.766590 AGAAAAACCGGATTATCCATTCCT 58.233 37.500 9.46 2.42 35.91 3.36
457 460 6.294010 GCTAGAAAAACCGGATTATCCATTCC 60.294 42.308 9.46 0.44 35.91 3.01
458 461 6.294010 GGCTAGAAAAACCGGATTATCCATTC 60.294 42.308 9.46 2.77 35.91 2.67
459 462 5.535030 GGCTAGAAAAACCGGATTATCCATT 59.465 40.000 9.46 2.08 35.91 3.16
460 463 5.070685 GGCTAGAAAAACCGGATTATCCAT 58.929 41.667 9.46 0.00 35.91 3.41
461 464 4.457466 GGCTAGAAAAACCGGATTATCCA 58.543 43.478 9.46 0.00 35.91 3.41
462 465 3.497262 CGGCTAGAAAAACCGGATTATCC 59.503 47.826 9.46 0.14 43.23 2.59
463 466 4.727235 CGGCTAGAAAAACCGGATTATC 57.273 45.455 9.46 0.58 43.23 1.75
470 473 4.211374 CAGATTATCCGGCTAGAAAAACCG 59.789 45.833 0.00 0.00 46.50 4.44
471 474 5.365619 TCAGATTATCCGGCTAGAAAAACC 58.634 41.667 0.00 0.00 0.00 3.27
472 475 6.147985 GGATCAGATTATCCGGCTAGAAAAAC 59.852 42.308 0.00 0.00 36.34 2.43
473 476 6.231211 GGATCAGATTATCCGGCTAGAAAAA 58.769 40.000 0.00 0.00 36.34 1.94
474 477 5.794894 GGATCAGATTATCCGGCTAGAAAA 58.205 41.667 0.00 0.00 36.34 2.29
475 478 5.407407 GGATCAGATTATCCGGCTAGAAA 57.593 43.478 0.00 0.00 36.34 2.52
507 510 6.806249 CACACATAAAGCGTGTATCCATTTTT 59.194 34.615 0.00 0.00 45.63 1.94
508 511 6.150307 TCACACATAAAGCGTGTATCCATTTT 59.850 34.615 0.00 0.00 45.63 1.82
509 512 5.645929 TCACACATAAAGCGTGTATCCATTT 59.354 36.000 0.00 0.00 45.63 2.32
510 513 5.182487 TCACACATAAAGCGTGTATCCATT 58.818 37.500 0.00 0.00 45.63 3.16
511 514 4.765273 TCACACATAAAGCGTGTATCCAT 58.235 39.130 0.00 0.00 45.63 3.41
512 515 4.195225 TCACACATAAAGCGTGTATCCA 57.805 40.909 0.00 0.00 45.63 3.41
513 516 4.630069 ACTTCACACATAAAGCGTGTATCC 59.370 41.667 0.00 0.00 45.63 2.59
514 517 5.779806 ACTTCACACATAAAGCGTGTATC 57.220 39.130 0.00 0.00 45.63 2.24
515 518 6.203915 TCAAACTTCACACATAAAGCGTGTAT 59.796 34.615 0.00 0.00 45.63 2.29
516 519 5.524281 TCAAACTTCACACATAAAGCGTGTA 59.476 36.000 0.00 0.00 45.63 2.90
518 521 4.843147 TCAAACTTCACACATAAAGCGTG 58.157 39.130 0.00 0.00 40.32 5.34
519 522 5.065988 ACTTCAAACTTCACACATAAAGCGT 59.934 36.000 0.00 0.00 0.00 5.07
520 523 5.510671 ACTTCAAACTTCACACATAAAGCG 58.489 37.500 0.00 0.00 0.00 4.68
527 530 8.770828 GCTAGTTAATACTTCAAACTTCACACA 58.229 33.333 0.00 0.00 35.23 3.72
528 531 8.770828 TGCTAGTTAATACTTCAAACTTCACAC 58.229 33.333 0.00 0.00 35.23 3.82
529 532 8.896320 TGCTAGTTAATACTTCAAACTTCACA 57.104 30.769 0.00 0.00 35.23 3.58
532 535 9.331106 GCTTTGCTAGTTAATACTTCAAACTTC 57.669 33.333 0.00 0.00 34.67 3.01
533 536 9.067986 AGCTTTGCTAGTTAATACTTCAAACTT 57.932 29.630 0.00 0.00 36.99 2.66
534 537 8.622948 AGCTTTGCTAGTTAATACTTCAAACT 57.377 30.769 0.00 0.00 36.99 2.66
535 538 9.118236 CAAGCTTTGCTAGTTAATACTTCAAAC 57.882 33.333 0.00 0.00 38.25 2.93
536 539 9.062524 TCAAGCTTTGCTAGTTAATACTTCAAA 57.937 29.630 0.00 0.00 38.25 2.69
537 540 8.615878 TCAAGCTTTGCTAGTTAATACTTCAA 57.384 30.769 0.00 0.00 38.25 2.69
538 541 7.878127 ACTCAAGCTTTGCTAGTTAATACTTCA 59.122 33.333 0.00 0.00 38.25 3.02
539 542 8.171840 CACTCAAGCTTTGCTAGTTAATACTTC 58.828 37.037 0.00 0.00 38.25 3.01
540 543 7.361286 GCACTCAAGCTTTGCTAGTTAATACTT 60.361 37.037 13.22 0.00 38.25 2.24
541 544 6.092807 GCACTCAAGCTTTGCTAGTTAATACT 59.907 38.462 13.22 0.00 38.25 2.12
542 545 6.092807 AGCACTCAAGCTTTGCTAGTTAATAC 59.907 38.462 19.98 0.30 44.82 1.89
543 546 6.173339 AGCACTCAAGCTTTGCTAGTTAATA 58.827 36.000 19.98 0.00 44.82 0.98
544 547 5.006386 AGCACTCAAGCTTTGCTAGTTAAT 58.994 37.500 19.98 0.00 44.82 1.40
545 548 4.389374 AGCACTCAAGCTTTGCTAGTTAA 58.611 39.130 19.98 0.00 44.82 2.01
546 549 4.008074 AGCACTCAAGCTTTGCTAGTTA 57.992 40.909 19.98 0.00 44.82 2.24
547 550 2.856222 AGCACTCAAGCTTTGCTAGTT 58.144 42.857 19.98 0.00 44.82 2.24
548 551 2.557920 AGCACTCAAGCTTTGCTAGT 57.442 45.000 19.98 8.22 44.82 2.57
552 555 4.164294 CAAAGATAGCACTCAAGCTTTGC 58.836 43.478 12.71 12.71 43.70 3.68
553 556 4.082895 AGCAAAGATAGCACTCAAGCTTTG 60.083 41.667 0.00 0.00 43.70 2.77
554 557 4.077822 AGCAAAGATAGCACTCAAGCTTT 58.922 39.130 0.00 0.00 43.70 3.51
555 558 3.683802 AGCAAAGATAGCACTCAAGCTT 58.316 40.909 0.00 0.00 43.70 3.74
557 560 3.190118 ACAAGCAAAGATAGCACTCAAGC 59.810 43.478 0.00 0.00 0.00 4.01
558 561 4.453478 TCACAAGCAAAGATAGCACTCAAG 59.547 41.667 0.00 0.00 0.00 3.02
559 562 4.388485 TCACAAGCAAAGATAGCACTCAA 58.612 39.130 0.00 0.00 0.00 3.02
560 563 3.999001 CTCACAAGCAAAGATAGCACTCA 59.001 43.478 0.00 0.00 0.00 3.41
561 564 4.248859 TCTCACAAGCAAAGATAGCACTC 58.751 43.478 0.00 0.00 0.00 3.51
562 565 4.020751 TCTCTCACAAGCAAAGATAGCACT 60.021 41.667 0.00 0.00 0.00 4.40
563 566 4.248859 TCTCTCACAAGCAAAGATAGCAC 58.751 43.478 0.00 0.00 0.00 4.40
564 567 4.541973 TCTCTCACAAGCAAAGATAGCA 57.458 40.909 0.00 0.00 0.00 3.49
565 568 5.869753 TTTCTCTCACAAGCAAAGATAGC 57.130 39.130 0.00 0.00 0.00 2.97
566 569 6.073548 ACGTTTTCTCTCACAAGCAAAGATAG 60.074 38.462 0.00 0.00 0.00 2.08
567 570 5.758296 ACGTTTTCTCTCACAAGCAAAGATA 59.242 36.000 0.00 0.00 0.00 1.98
568 571 4.576463 ACGTTTTCTCTCACAAGCAAAGAT 59.424 37.500 0.00 0.00 0.00 2.40
569 572 3.938963 ACGTTTTCTCTCACAAGCAAAGA 59.061 39.130 0.00 0.00 0.00 2.52
570 573 4.278678 ACGTTTTCTCTCACAAGCAAAG 57.721 40.909 0.00 0.00 0.00 2.77
571 574 5.353123 ACTTACGTTTTCTCTCACAAGCAAA 59.647 36.000 0.00 0.00 0.00 3.68
572 575 4.873827 ACTTACGTTTTCTCTCACAAGCAA 59.126 37.500 0.00 0.00 0.00 3.91
573 576 4.439057 ACTTACGTTTTCTCTCACAAGCA 58.561 39.130 0.00 0.00 0.00 3.91
574 577 5.405331 AACTTACGTTTTCTCTCACAAGC 57.595 39.130 0.00 0.00 0.00 4.01
575 578 9.931210 AAATTAACTTACGTTTTCTCTCACAAG 57.069 29.630 0.00 0.00 34.59 3.16
576 579 9.710979 CAAATTAACTTACGTTTTCTCTCACAA 57.289 29.630 0.00 0.00 34.59 3.33
577 580 8.885722 ACAAATTAACTTACGTTTTCTCTCACA 58.114 29.630 0.00 0.00 34.59 3.58
578 581 9.155053 CACAAATTAACTTACGTTTTCTCTCAC 57.845 33.333 0.00 0.00 34.59 3.51
579 582 8.885722 ACACAAATTAACTTACGTTTTCTCTCA 58.114 29.630 0.00 0.00 34.59 3.27
597 600 9.649167 GTCAGGTACATTAGTAGTACACAAATT 57.351 33.333 2.52 0.00 42.73 1.82
598 601 9.032624 AGTCAGGTACATTAGTAGTACACAAAT 57.967 33.333 2.52 0.00 42.73 2.32
599 602 8.413309 AGTCAGGTACATTAGTAGTACACAAA 57.587 34.615 2.52 0.00 42.73 2.83
600 603 8.413309 AAGTCAGGTACATTAGTAGTACACAA 57.587 34.615 2.52 0.00 42.73 3.33
601 604 8.413309 AAAGTCAGGTACATTAGTAGTACACA 57.587 34.615 2.52 0.00 42.73 3.72
602 605 7.972832 GGAAAGTCAGGTACATTAGTAGTACAC 59.027 40.741 2.52 0.00 42.73 2.90
603 606 7.670979 TGGAAAGTCAGGTACATTAGTAGTACA 59.329 37.037 2.52 0.00 42.73 2.90
604 607 8.059798 TGGAAAGTCAGGTACATTAGTAGTAC 57.940 38.462 0.00 0.00 40.78 2.73
605 608 7.892241 ACTGGAAAGTCAGGTACATTAGTAGTA 59.108 37.037 0.00 0.00 38.98 1.82
606 609 6.724905 ACTGGAAAGTCAGGTACATTAGTAGT 59.275 38.462 0.00 0.00 38.98 2.73
607 610 7.036220 CACTGGAAAGTCAGGTACATTAGTAG 58.964 42.308 0.00 0.00 38.98 2.57
608 611 6.573680 GCACTGGAAAGTCAGGTACATTAGTA 60.574 42.308 0.00 0.00 38.98 1.82
609 612 5.794894 CACTGGAAAGTCAGGTACATTAGT 58.205 41.667 0.00 0.00 38.98 2.24
610 613 4.631813 GCACTGGAAAGTCAGGTACATTAG 59.368 45.833 0.00 0.00 38.98 1.73
611 614 4.286032 AGCACTGGAAAGTCAGGTACATTA 59.714 41.667 0.00 0.00 38.98 1.90
612 615 3.073062 AGCACTGGAAAGTCAGGTACATT 59.927 43.478 0.00 0.00 38.98 2.71
613 616 2.639839 AGCACTGGAAAGTCAGGTACAT 59.360 45.455 0.00 0.00 38.98 2.29
614 617 2.047061 AGCACTGGAAAGTCAGGTACA 58.953 47.619 0.00 0.00 38.98 2.90
615 618 2.841442 AGCACTGGAAAGTCAGGTAC 57.159 50.000 0.00 0.00 38.98 3.34
616 619 3.118038 ACAAAGCACTGGAAAGTCAGGTA 60.118 43.478 0.00 0.00 38.98 3.08
617 620 2.301346 CAAAGCACTGGAAAGTCAGGT 58.699 47.619 0.00 0.00 38.98 4.00
618 621 2.033801 CACAAAGCACTGGAAAGTCAGG 59.966 50.000 0.00 0.00 38.98 3.86
619 622 2.684881 ACACAAAGCACTGGAAAGTCAG 59.315 45.455 0.00 0.00 40.40 3.51
620 623 2.722094 ACACAAAGCACTGGAAAGTCA 58.278 42.857 0.00 0.00 0.00 3.41
621 624 4.275936 ACATACACAAAGCACTGGAAAGTC 59.724 41.667 0.00 0.00 0.00 3.01
622 625 4.207165 ACATACACAAAGCACTGGAAAGT 58.793 39.130 0.00 0.00 0.00 2.66
623 626 4.836125 ACATACACAAAGCACTGGAAAG 57.164 40.909 0.00 0.00 0.00 2.62
624 627 5.590530 AAACATACACAAAGCACTGGAAA 57.409 34.783 0.00 0.00 0.00 3.13
625 628 6.701145 TTAAACATACACAAAGCACTGGAA 57.299 33.333 0.00 0.00 0.00 3.53
626 629 6.320164 ACTTTAAACATACACAAAGCACTGGA 59.680 34.615 0.00 0.00 32.44 3.86
627 630 6.417635 CACTTTAAACATACACAAAGCACTGG 59.582 38.462 0.00 0.00 32.44 4.00
628 631 6.972328 ACACTTTAAACATACACAAAGCACTG 59.028 34.615 0.00 0.00 32.44 3.66
629 632 7.095695 ACACTTTAAACATACACAAAGCACT 57.904 32.000 0.00 0.00 32.44 4.40
630 633 7.911205 TGTACACTTTAAACATACACAAAGCAC 59.089 33.333 0.00 0.00 32.44 4.40
631 634 7.986562 TGTACACTTTAAACATACACAAAGCA 58.013 30.769 0.00 0.00 32.44 3.91
632 635 8.844441 TTGTACACTTTAAACATACACAAAGC 57.156 30.769 0.00 0.00 32.44 3.51
633 636 9.997482 ACTTGTACACTTTAAACATACACAAAG 57.003 29.630 0.00 0.00 34.80 2.77
669 672 8.779303 CCGAATATGTAAATACAACAATAGGCA 58.221 33.333 0.00 0.00 39.99 4.75
670 673 8.780249 ACCGAATATGTAAATACAACAATAGGC 58.220 33.333 0.00 0.00 39.99 3.93
674 677 7.918562 GCCAACCGAATATGTAAATACAACAAT 59.081 33.333 0.00 0.00 39.99 2.71
675 678 7.121463 AGCCAACCGAATATGTAAATACAACAA 59.879 33.333 0.00 0.00 39.99 2.83
676 679 6.600032 AGCCAACCGAATATGTAAATACAACA 59.400 34.615 0.00 0.00 39.99 3.33
677 680 7.023197 AGCCAACCGAATATGTAAATACAAC 57.977 36.000 0.00 0.00 39.99 3.32
678 681 7.337184 TCAAGCCAACCGAATATGTAAATACAA 59.663 33.333 0.00 0.00 39.99 2.41
679 682 6.824196 TCAAGCCAACCGAATATGTAAATACA 59.176 34.615 0.00 0.00 40.98 2.29
703 706 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
704 707 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
705 708 3.386078 TGCTCTCTCTCTCTCTCTCTCTC 59.614 52.174 0.00 0.00 0.00 3.20
706 709 3.378512 TGCTCTCTCTCTCTCTCTCTCT 58.621 50.000 0.00 0.00 0.00 3.10
707 710 3.494048 CCTGCTCTCTCTCTCTCTCTCTC 60.494 56.522 0.00 0.00 0.00 3.20
892 908 0.684535 GGGTTTGTGGGAAATGGGTG 59.315 55.000 0.00 0.00 0.00 4.61
893 909 0.472925 GGGGTTTGTGGGAAATGGGT 60.473 55.000 0.00 0.00 0.00 4.51
894 910 0.472734 TGGGGTTTGTGGGAAATGGG 60.473 55.000 0.00 0.00 0.00 4.00
933 950 2.117423 GGAGTGGTTGGGGTTGGG 59.883 66.667 0.00 0.00 0.00 4.12
934 951 2.282180 CGGAGTGGTTGGGGTTGG 60.282 66.667 0.00 0.00 0.00 3.77
935 952 2.282180 CCGGAGTGGTTGGGGTTG 60.282 66.667 0.00 0.00 0.00 3.77
936 953 4.280019 GCCGGAGTGGTTGGGGTT 62.280 66.667 5.05 0.00 41.21 4.11
938 955 3.583882 AATGCCGGAGTGGTTGGGG 62.584 63.158 5.05 0.00 41.21 4.96
1222 1268 2.342279 CTGGAGAAACACGGCGGA 59.658 61.111 13.24 0.00 0.00 5.54
1246 1292 4.821589 CTTGAGAGCCCCGTCCGC 62.822 72.222 0.00 0.00 0.00 5.54
1356 1411 4.188247 TGACAATACCTTCTGGAACTCG 57.812 45.455 0.00 0.00 37.04 4.18
1373 3788 8.572185 TCAATCGAAGGAAATGTTATTTTGACA 58.428 29.630 0.00 0.00 0.00 3.58
1451 5011 6.706716 TGGTAGACATGTGAATTTTGTTCGTA 59.293 34.615 1.15 0.00 0.00 3.43
1515 5095 7.441836 TGAACTCACATGAAACACTACACTAT 58.558 34.615 0.00 0.00 0.00 2.12
1564 5144 3.243434 ACGACGGACATGAGTATGGAATC 60.243 47.826 0.00 0.00 38.66 2.52
1582 5162 2.553079 TTCAGCAAAACCACAACGAC 57.447 45.000 0.00 0.00 0.00 4.34
1693 5273 0.249657 GCAGGATGAAGGGCGTAGAG 60.250 60.000 0.00 0.00 39.69 2.43
1801 5381 5.163513 GGAATGACAACAAAGCAAGGTATG 58.836 41.667 0.00 0.00 0.00 2.39
1946 5526 8.518430 ACCAATAATGTGCACAAGATATACAA 57.482 30.769 25.72 0.00 0.00 2.41
2031 5611 1.963515 ACAACAATCAAGGTTCCTGCC 59.036 47.619 0.00 0.00 0.00 4.85
2033 5613 5.009854 ACAAACAACAATCAAGGTTCCTG 57.990 39.130 0.00 0.00 0.00 3.86
2273 5856 4.346730 AGGCATCTGATTGGTCAATTGAA 58.653 39.130 10.35 0.00 33.05 2.69
2299 5882 7.259088 ACTAGGTTTTCACTGGTGATCTATT 57.741 36.000 4.19 0.00 39.64 1.73
2348 5931 2.158325 ACCCAATCACAACAATCCCAGT 60.158 45.455 0.00 0.00 0.00 4.00
2357 5940 7.319646 TGAATAAATTGCTACCCAATCACAAC 58.680 34.615 0.00 0.00 43.22 3.32
2369 5952 8.756927 TGGTGGATTTCAATGAATAAATTGCTA 58.243 29.630 0.00 0.00 37.44 3.49
2411 5994 1.969923 CAACCCAGCCCTTTGAAATCA 59.030 47.619 0.00 0.00 0.00 2.57
2498 6081 9.777575 TTCACTAAAACAAAGCACTAAGTTTAC 57.222 29.630 0.00 0.00 33.45 2.01
2544 6127 4.927425 TGCTACCGACTTGAATAGTTGAAC 59.073 41.667 0.00 0.00 40.23 3.18
2570 6176 6.906143 GTGTCGACTACTCTACATATCACAAC 59.094 42.308 17.92 0.00 0.00 3.32
2637 6243 8.543774 ACTTCTACAGAAATGACATGGAGTAAT 58.456 33.333 0.00 0.00 33.07 1.89
2664 6270 0.773644 AGCATGTGTCCTCCAAAGGT 59.226 50.000 0.00 0.00 43.82 3.50
2707 6313 2.622962 GCCGAAACCCCGTGAAAGG 61.623 63.158 0.00 0.00 0.00 3.11
2725 6331 4.402056 TTTAGGAATAGCTGAAGGGACG 57.598 45.455 0.00 0.00 0.00 4.79
2850 6456 4.516698 GCAATCATCCCCACAATAGTAGTG 59.483 45.833 0.00 0.00 36.76 2.74
2857 6463 5.011329 GTCATTATGCAATCATCCCCACAAT 59.989 40.000 0.00 0.00 34.22 2.71


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.